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Defining Color in LogoGenerator

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jukri:
Is it possible to add a color feature for the LogoGenerator function in FeatureReduce? I would like to e.g have a C nucleotide colored in different shades of blue, depending on the experimental condition it came from?

Thanks

xiangjun:
Hi,

Thanks for being the first to ask questions on the Forum! I'd like to clarify that the LogoGenerator utility is within the REDUCE Suite, which is a completely separate package from FeatureReduce.

As to your question of coloring some Cs (or other bases) in separately color, the answer is no, at least in the current version of LogoGenerator. The DNA/RNA logos, as I am aware of, consist of 4 different bases, as shown in the 4 columns of a PWM or PSAM. To color certain bases differently, such info must be specified in some way in the file, which will break the format.

There are so many logo generators available. Maybe some of them are more advanced than the functionality LogoGenerator currently provides, and can do what you are asking for.

If you want to generate only a fews logos, you could use LogoGenerator to generate the logos in EPS format. Then using Adobe Illustrator, you can edit/modify as you see fit.

Hope this helps.

Xiang-Jun

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